We have undertaken a program that is aimed at determining, on a molecular level, those genetic alterations in primary breast tumor DNA that have a statistically significant association with the patients history, characteristics of the tumor, and the patients prognosis. The most frequent type of mutation is loss of heterozygosity (LOH) at specific regions of the cellular genome in tumor DNA. During the past year we have identified four new regions of the genome which are affected by LOH in primary human breast tumors. Three of these are located on chromosome 6q, one between markers D6S268 and D6S261 (6q14- q16.2), another between D6S268 and D6S261 (6q16.3-q23) and the third between D6S287 and D6S270 (6q22.3-q23.1). We have shown that the human homolog of the mouse mammary tumor gene Int6 is located on chromosome 8q22-q23, 6.6 cM centromeric of D8S344. Using a polymorphic marker within the Int6 gene we have detected LOH in 28% of 39 informative primary human breast carcinomas. We are currently determining whether the remaining allele in these tumors contains a point mutation. To identify the target gene for LOH on chromsome 17q12-q21 in sporadic breast carcinomas we have collaborated with Dr. Ray White (University of Utah) and Dr. Bruce Ponder (University of Cambridge) to develop a physical map of the region. Using polymorphic markers from this region we were able to show that the 120-150 kb interval between D17S846 and D17S746 represents the smallest common region which is deleted. We are currently studying two overlapping P1 phage clones which spans this region and have found two candidate target genes which are being examined for point mutations.